31 March 2014

When I was on the academic job market, I read somewhere that successful applicants sent out around sixty applications.

That was pretty much in line with my experience. I think I sent out over fifty applications before I got the phone interview that ultimately led to this job. And because of the delays, I ended up sending out more applications after I had done the on-site interview.

It’s a frustrating process, because there’s no progress bar. You send this off, and you rarely have any idea of when it’s received, whether a shortlist has been made, or when a decision is expected.

I was surprised by how many applications just... vanished. Many search committees didn’t feel compelled to inform candidates of the outcome. Not even a simple, “No thank you.”

I think it starts to suck hard somewhere around the forty mark. Particularly if none of them has even yielded a lead, like an on-site interview.

The job market wasn’t great when I was in it, and it’s probably worse now. This means that you have to be ready to take a lot of rejection.

But the moral of the story is that the number of noes is almost irrelevant. Because all it takes is one “Yes.”

Why is this making the news rounds today? Because the person pointing out the savings, Suvir Mirchandani, is a teenager. News agencies, and the public, love “teen genius” stories. See Jack Andraka (cancer test), Boyan Slat (ocean clean-up) and Aidan Dwyer (solar power).

(Off the top of my head, I can’t think of many teenage girls who have achieved similar press coverage).

All of these teens put out a flashy claim that... well... remains to be seen if it will yield anything interesting. But I see their stories circulating in social media for years.

This is a great example of the power of narrative. People love underdog stories, and teens are underdogs in almost every way. People want to believe that teens can make big breakthroughs in science and technology, and I think a lot of critical appraisal is dialed down, if not shut off.

I doubt any of these stories would have received much media attention if the person making the claim was 20 or older.

Update, 1 April 2014: Oh, as I might have expected: the flashy claim from Mirchandani is being criticized.

Luis Colom, a professor at University of Texas Brownsville, has died from cancer.

Dr. Colom and I were hired the same year, 2001. I was hired by The University of Texas-Pan American. Dr. Colom was hired down the road at University of Texas-Brownsville.

We both did neuroscience. I think it’s fair to say we were the first people doing neuroscience in the Lower Rio Grande Valley. But despite this, we never had any serious interactions. This was probably because his research was distinctly biomedical and mammalian, whereas mine is emphatically not. I think I saw him make some opening remarks at an NSF workshop I attended at Brownsville.

A missed opportunity.

This message from UT Brownsville makes it clear he did a lot for their institution. I once heard that he had been denied tenure at another institution. I have no idea if that’s correct, but if it is, it certainly is a lesson in how people can not make it in one place, but do well in another.

It’s shame he did not live to see the opening of The University of Texas Rio Grande Valley. Because he was obviously the sort of person who helped make that transition possible, and he would probably have enjoyed the challenge of working in a new university.

Update, 13 May 2014: Another thing we had in common was a student, Nadia Carreon. Nadia worked with me as an undergraduate, and Dr. Colom as a master’s student. Nadia and I were working on our second paper together when Dr. Colom died, so we dedicated the paper to his memory.

27 March 2014

I mentioned a while back that I was up to my eyeballs in writing. Between Christmas Eve and mid March, I submitted seven pieces of academic writing to editors.

In the past two weeks, I’ve had two of those article accepted for publication. This make me very happy. What has made me happier was that they were accepted without revisions. Papers accepted “as is” are the baby pigeons of academia: you know that logically they must exist, but you might go your whole life without seeing one.

And the editor’s comments made me bounce up and down. First this:

I don’t know when I have enjoyed reading a paper so much!

Then this:

I have to say that I am not often in the position of having no changes to suggest, but I really like the piece and don’t want to muck with it.

What’s the secret? These two papers had an advantage: neither was a data-driven, experimental paper with original research. That made the reviewing process easier.

I post this not to gloat. (Well, not just to goat, I guess. A teensy little bit of gloating.) You know, scientific publishing is so often so long and so hard, that I just felt compelled to point out that occasionally, you win one.

25 March 2014

On the CRUST-L discussion list, Daniel Abed-Navandi shared this picture. He stumbled upon this large flat isopod clinging to the mantle of a squid he was prepping for the dinner plate. He suspects is belong to Seroloidea.

21 March 2014

Currently blowing up my twitter feed are responses to two graphical abstracts in the Journal of Proteomics, both published a couple of years ago in 2012. (There is no statute of limitations on poor decisions.)

Honey, sweet honey? Chestnut, acacia, sunflower, eucalyptus, orange, you name it. Just the same. Eat any of them, you will be savouring animal, not plant proteins!

Um. Er. I think the word “inappropriate” is overused, I can’t find a better one here. Those are inappropriate.

I went looking through the graphic abstracts in the journal since then. I saw no other examples of similar pictures with a quick skim.

There is a common denominator to both papers besides the style of the graphical abstracts. The author for correspondence on both is Pier Giorgio Righetti, who is on the journal’s editorial board (thanks to Ted Morrow for spotting that). Alfonsina D'Amato is also listed as an author on both paper, but that Righetti sits on the editorial board of the journal makes his involvement more noteable.

Rajini Rao reached out to Dr. Righetti about the first of these graphical abstracts, and got this response:

Hello Prof. Rao,

I wonder if you have been trained in the Vatican. As you claim to be a professor of Physiology, let me alert you that this image is physiology at its best!

Bug has emailed to see if permission was given to use this. Photographer Alex Wild noted that this might be the thing that lands the authors in trouble, if the photographer did not give permission for this image to be used. The musicians in the image might have less power than the photographer in this case.

This is clearly going to be an evolving story, so I expect to update this post a few times. For one, Hysell Oviedo has asked Elsevier representative Tom Reller for a response. He justtweeted:

We're addressing this right now.

Hat tip to several people who alerted me of these papers: Michael Hawkes, Hysell Oviedo, Karl Broman, and Jon Tennant. Apologies to those I missed who brought this to attention. (Update: It seems TOC ROFL Tumblr, Jillian Buriak, Jonathan Eisen played a lead in bringing this to attention.)

Additional: Amidst Science beat me to finding additional graphic abstracts from the Righetti lab. First, we have here (Journal of Proteomics again, “Cibacron Blue and proteomics: The mystery of the platoon missing in action”). (Update: Tom Reller says this one will also be removed.)

Yves Klein made it to the Olympus of modern artists with Cibacron Blue in his glamorous Blue Venus, whereas we scientists made a “blue fiasco”. Yet, redemption is sculptured inside!

Even more additional: Righetti’s unconventional use of graphical abstracts is not limited to pictures of women. Journal of Proteomics, again, “Popeye strikes again: The deep proteome of spinach leaves”:

Popeye kept gulping down large amounts of spinaches to become the first iron-man of America, not knowing that spinach leaves would comprise not less than 322 proteins as listed therein.

Perhaps the winner of the EuroKUP contest, as set up by A. Vlau in Athens (modern Olympic games?), but read the paper and cast your vote!

This one (from here, “Identification of olive (Olea europaea) seed and pulp proteins by nLC-MS/MS via combinatorial peptide ligand libraries”) is a benign image, but the caption is strange:

The sacred fruit to Athena here reveals its secret proteome: 61 proteins in the stone and 231 unique gene products in the pulp. Will this save Greece from default?

More weirdness in Journal of Proteomics, “Poppea's bath liquor: The secret proteome of she-donkey's milk”:

Two Buridan's asses between two hay stacks, unable to decide, died of starvation. She-donkeys are not so dumb, as their milk is nutritious, hypoallergenic, with cosmetic properties (ask Poppea).

And when you get to the paper, “Ginger Rogers? No, Ginger Ale and its invisible proteome,” the inevitable conclusion is that Righetti does not take graphical abstracts seriously.

Ginger Ale or Ginger Rogers? Even though we might be going against our findings reported inside, we confess that we much prefer the latter! Chapeau to her, in fact “Top Hat” to the fabulous duo Ginger and Fred.

Thanks for kindly letting me know that a graphical abstract published in Journal of Proteomics is getting unwelcome publicity. Although I, personally, so not think that the alluded images are sexist (as well as I would not consider it sexist if a man were represented), at least this was neither the intention of the authors nor of the editor, I cn (sic) agree that this kind of images may be inappropriate for illustrating a scientific paper, and consequently have asked our journal manager to remove them. If anyone has been offended, officially apologize for that, and I hope to give settle the case as soon as possible to devote to the lab which is what take take me up most of the day.

Best
Juan

If someone calls your images sexist, and you agree to take them down, you are not helping your case if you say, “But I didn’t think they were sexist.”

A Graphical abstract is mandatory for this journal. It should summarize the contents of the article in a concise, pictorial form designed to capture the attention of a wide readership online. Authors must provide images that clearly represent the work described in the article.

These captured the attention of readers, all right.... but these didn’t even meet the journal’s own technical specifications. It asks for images that are at least 531 × 1328 pixels. None of the contentious images above come even close to 1,000 pixels in size.

Award-winning additional: Sarcastic F notes Righetti won a substantial award, the first Beckman Award, in 2012. Author Frantisek Svec specifically singles out the paper featured at the top of the post with the worst graphical abstract:

During his scientific career, he published over 750 papers, many of them with very catchy titles. For example, his recent papers in the Journal of Proteomics are entitled “Harry Belafonte and the secret of proteome in coconut milk” and “‘Cheek-to-cheek’ urinary proteome profiling via combinatorial peptide ligand libraries: A novel, unexpected elution system”. Wouldn’t you open a paper with such a title right away? No wonder that papers with these titles are widely referred and led to almost 20 000 citations.

You may now proceed to chew on how that sort of scientific clout affects the willingness of others to point out, “That may not be a good idea.”

Update, 24 March 2014: The three papers are now available on ScienceDirect again, minus the graphical abstracts. Dr. Righetti is no longer listed as being a member of the Journal of Proteomics editorial board.

I am not surprised that our current president, Robert Nelsen, is one of the finalists. I am surprised by the journalism on display, since the names of these individuals were secret until yesterday. And that secrecy is the main section of the story.

In a news release earlier this month, the UT System public affairs office explained the strategy — which was employed in recent presidential searches at UT Arlington, UT Health Science Center - Houston and UT MD Anderson — as a way to better attract top-tier talent.

"Names of candidates are kept confidential to attract the absolute highest quality of candidates," the release read. "Executive search firms advise that top candidates are reluctant to pursue a position without a promise of confidentiality, as it may jeopardize their current positions." ...

After UTPA President Robert Nelsen and his predecessor, Blandina "Bambi" Cárdenas, made open campus visits prior to their hirings, faculty members have become accustomed to meeting their leaders before their hiring.

“We’ve had all this emphasis on community involvement,” said Dora Saavedra, a member of the UTPA faculty senate. “It seems very odd that the inclusivity will be discontinued, or seems that it will be discontinued with the new university.” ...

(University of Texas Chancellor) Cigarroa contacted Sanchez on Monday, asking not to publish the names, as the UT System had promised to protect candidates’ identities and making them public could negatively impact the hiring. But the editor decided public interest in identifying the candidates — thus allowing a public vetting — trumped UT System’s desire to keep the process hushed.

17 March 2014

“For better or worse,” said Steven A. Edwards, a policy analyst at the American Association for the Advancement of Science, “the practice of science in the 21st century is becoming shaped less by national priorities or by peer-review groups and more by the particular preferences of individuals with huge amounts of money.”

Among other things, the article links the somewhat surprising decision of the American government to create the BRAIN Initiative to the interests of Microsoft co-founder Paul Allen, who created the Allen Institute out of his own personal interest in neuroscience. It also points out that there is a lot of interest by the super-rich in, wait for it, curing cancer and other diseases.

I can’t help but think about filmmaker Jim Cameron going to the deepest point in the ocean. Cameron was able to do it because he had a lot of money, so he went instead of working scientists. Are we moving back to a time when only the rich get to be scientists? I hope not.

A super quick reaction is that this is another reason why I think science crowdfunding is important. When lots of people can pool their resources to support research projects, it could be a democratizing counter to single rich people setting the research agenda.

14 March 2014

When I go to the movies, I sit to the very end. The last frame. I do this because I love love love it when filmmakers put little Easter eggs at the end of the credits, and because I love film music, and I just think, darnit, these people worked hard and someone should see their names on the big screen.

The last few years, something I’ve seen more of in the end credits of movies are “Production babies.” It’s the names of babies had by staffers during the production of the movie. Pixar pioneered the practice with Toy Story in 1995.

We should do this in scientific papers. Routinely. Put a mention of it in the acknowledgements section. Editors usually give authors a fair amount of freedom to thank whoever they want.

There’s a lot of talk and research about how families affect academic careers, especially scientific ones (“For men, having children is a career advantage. For women, it’s a career killer”). Listing “science babies” born during the making of a scientific paper might be a way to show in the research community that having children is not only normal, but worth celebrating.

12 March 2014

“Does this invertebrate animal feel pain?” As Noah Gray noted, mass media seems to cover some version of this question about every six months or so.

This time, we have an article that appeared a few weeks ago from New Scientist. It’s just been picked up in The Washington Post and a Popular Scienceblog. The piece features the work of Robert Elwood, Robyn Crook (both of who have appeared on the blog before) and Hans Smid.

It’s an extremely good article that captures a lot of the nuances of the issue. I was surprised, though, to read this paragraph describing Elwood’s work:

(Elwood) started with prawns. After so many years of working with them, he thought he knew what to expect, which was that he would see nothing more than reflex reactions. But to his surprise, when he brushed acetic acid on their antennae, they began grooming the treated antennae with complex, prolonged movements of both front legs. What’s more, the grooming diminished when local anesthetic was applied beforehand.

Elwood is describing work he co-authored back in 2007 (Barr et al., 2007). What this fails to mention is that this effect could not be replicated in other species (Puri and Faulkes 2010). Elwood knows this; he’s mentioned the failure to replicate in his academic papers (Elwood 2011, page 177):

I’m curious as to whether this was mentioned during the interview, or was removed to get the article to the appropriate word count.

How should scientists, and reporters, discuss work that has failed to replicate? The original Barr and colleagues article remains in the scientific literature; failed replication alone is not grounds for retraction. In that sense, the paper by Barr and company has not been definitively shown to be flawed or wrong. But being able to replicate effects is an acid test (no pun intended) for determining if those effects are real and robust.

Reporters often go after quotes from outside experts; “scientists who were not involved in the study.” This is good practice, and represents due diligence on the part of the reporter to find potentially critical viewpoints. But these external experts are often working from their knowledge of the field, and are generating critiques from theory and first principles. It’s not common for them to have done any experiments.

If it’s good practice to get responses from other researcher making criticisms with no data, surely it’s even better practice to talk about criticisms that are backed up with data published in peer reviewed journals?

The paragraph I quoted above also does not mention an interpretive problem. “Grooming” is the behaviour that is used to indicate nociception and/or pain in the shrimp. Acid causes an increase in grooming. Local anesthetic applied after acid reduces grooming. So far, so good.

What would you predict if you applied anesthetic alone?

The anesthetic should not be noxious – it is supposed to reduce sensory input, after all – so you might predict to see no increase in grooming compared to control.

I don’t know what to make of this, except that it complicates the story. The shrimp are clearly detecting the anesthetic and responding to it in the same way as the noxious stimuli: increased grooming.

Right, it’s more complicated than story can show. Chose to focus on evidence of Elwood’s total research, not one experiment.

I disagree with Stelling’s characterization of this being “one experiment.” The entire first paper by Barr and colleagues hinges on the notion that that acids and bases cause crustaceans to groom, and that is indicative of nociception.

Stelling’s answers point out the tension between a good narrative and scientific processes. For a journalistic narrative, uncertainty is uncertainty. There are no need for different gradations of uncertainty. The author of a study going, “It could be something else,” outside experts saying, “ don’t think so,” and sitting down and actually running the entire experiment again and not getting it to work all serve the same purpose in the narrative: saying, “maybe not.”

Scientifically, those forms of uncertainty are not at all equivalent.

Additional, 18 March 2014: Bio News Texas also reports on Crook and Elwood’s work. The article is apparently inspired by, but not a duplicate, of the New Scientist article.

10 March 2014

Ethics Bowl is a university competition at regional an national levels intended to get undergraduate students (mainly philosophy majors) to discuss ethical issues. I’ve helped with the preparation of teams from my university in the past.

One of my colleagues, Cynthia Jones, helped draft cases this year (available online here). One case involved a topic I suggested to her: “de-extinction,” which I’d seen via a TEDx symposium devoted to the topic, of which Carl Zimmer was one of the speakers. And it was used as one of the cases in the finals of the competition. The case read thus:

Gone today, here tomorrow

In Jurassic Park-like fashion, scientists have been attempting to bring recently-extincted species back from the dead, so to speak. The 5 April 2013 journal Science reported that the first live product of de-extinction, a Pyrenean ibex, lasted only a few minutes before extincting again. The ibex, which was produced by a process similar to that used for Dolly, the infamous cloned sheep, was driven to extinction in the first place with the help of humans. Some scientists think it only fitting that humans play a part in the de-extinction of those species that we helped to extinct in the first place.

An environmental argument for de-extinction arises from the case of the wooly mammoth, a species whose de-extinction would likely have beneficial consequences, such as the restoration of a more diverse ecology in the Arctic. Unfortunately for dinosaur enthusiasts, species of dinosaurs are not contenders for de-extinction at the moment, as the processes for de-extinction that are currently available require “fresher” DNA. And some notable environmental scientists are concerned about the unforeseen effects of reintroducing a de-extincted species into an environment, much like the unforeseen effects of introducing non-native species of plants or animals into novel environments. One might also wonder whether de-extincted creatures fall under endangered species laws and whether it is appropriate to use the term ‘extinct’ for species from this time forward, given that de-extinction is an imminent possibility.

Speaking of de-extinction, The Current radio show recently had a very good look at the passenger pigeon, which went extinct one hundred years ago this year. It is probably one of the better candidates for trying the technique.

Browsing the fifteen cases used at the national Ethics Bowl competition is interesting because of how many revolve around scientific and technologial issues.

Case #1 is called “Open Exce$$ Publishing,” and involves open access scientific publishing.

Case #3 is about Google Glass.

Case #4 is about drones.

Case #14 is about honeybee colony collapse and pesticides.

University of Montana won the national Ethics Bowl championship this year, beating the University of Oklahoma in the final round.

In the past few weeks on my other social media sites, I’ve been asking for help in getting UTPA into the finals of the Sixth Fan competition. Up for grabs was $100,000 in scholarship money. Given that we serve one of the poorest areas in the country, I reckoned we could put that scholarship money to better use than most universities.

We made it past the first round, then the elite eight, and into the final four. We started the final four with only 10% of the vote, but we managed to reduce the spread to only a few percentage points by yesterday.

I voted a lot, but it was not enough. We are not in the finals. Alas. But we came close. And given than we were against a university with much more “name” recognition (Brighman Young University), we were competitive.

07 March 2014

Recently, there has been a lot of discussion in the online science community about the data-sharing policies of PLOS journals, including PLOS ONE. I’ll link to DrugMonkey’s discussion here, as it was one of the first comments, and has one of the liveliest comment threads.

One reason this is contentious is because different scientists have different answers to the question, “Who owns research data?”

One view is that data is the property of the individual researchers, who, as owners, are allowed to use data in whatever way they see fit. (Whether students or lab leaders have greater claim to that data is another issue I’ll put aside for now.)

Others tend to view data as being in the public domain. Research, the argument goes, is paid for by government funding agencies, and taxpayers should have free and unfettered access to anything generated by tax dollars. (That not all is tax supported is another issue I’ll put aside for now.)

For many researchers, both of these views are wrong.

I checked my university’s Handbook of Operating Procedures on intellectual property. It clearly states that research data are considered intellectual property, and that we follow University of Texas System rules about intellectual property (“plain English” version here), which includes research data (section 3). And those rules are crystal clear:

I do not own research data I generate. Neither do the funding agencies.

Things get muddier because “scholarly works” – presumably journal article and books and papers – are owned by the authors.

While the Regents own the
data in principle, it seems individual researchers are left to their
own devices in practice. I doubt that the Regents care about how researchers choose to share data (or not), unless... it becomes possible to make money from data sets. It’s quite clear that the main aim of this policy is to allow the UT
System to profit financially from inventions and patents. If there is money to be made from university research, the UT System wants to be one of the ones making it.

The University of Texas System is not small potatoes, but I have no idea if similar policies exist in other institutions. I’d be interested to hear from people in the comments about their university’s intellectual property rules.

05 March 2014

When the new Texas university was announced, which we now know will be University of Texas Rio Grande Valley, the first thing I remember our Dean saying was something along the lines of, “Faculty will keep their jobs.”

Today, the University of Texas at Brownsville student paper is reporting that may not be the case.

Bobbette Morgan... asked lawyers at the UT System “if tenure at UTB and UTPA means tenure at UT-RGV” and was told “no.” ...

“Legally, that is a true statement, but the intention here is to grow the University of Texas-Rio Grande Valley into one of the larger universities,” Cigarroa said.

I myself am not worried about me, personally. My department is short of faculty as it is. But it is disconcerting to say the least to have heard one thing a little over a year ago, and another now. I think this question and concern is more relevant to University of Texas at Brownsville, where there have been multiple legal cases of the institution trying to dismiss tenured faculty.

Additional, 9 April 2014: In an email to faculty, advisor Julio Leon wrote (my emphasis):

In the coming weeks we will share specific processes for how UTB and
UTPA tenured and tenure-track faculty may choose to transition to
faculty positions at UTRGV.